Hi Matt
I'm not familiar with running Jmol from the command line, but a few things:
> $Jmol -ionx myscript.spt molecule.pdb
>
> and mysrcript.spt is:
>
> select all;
> write coords pdb one.pdb;
> select none;
>
> then one.pdb is created, but it is empty.
I think that you need to add the "-s" switch so that the script will be read.
Ii was me who added those examples in the Wiki, they were taken from a message
of Bob's
in the email list, and they are also shown as examples in the Scripting Doc
page, but the
simultaneous use of a script file + a molecule file is not documented anywhere.
I just tested
it and it works if you do
Jmol -ionxs myscript.spt molecule.pdb
(note the added "s")
> #Place measurement in variable dist
> dist=script("show measurements")
> then, dist14.txt is created, but is empty except for "Show measurements."
I'm not sure this should work. Do you have any doc supporting this script()
syntax?
> I suspect that Jmol is not loading the pdb file specified in the command
> $Jmol -ionx myscript.spt molecule.pdb
Yes, so it seems. Try
Jmol myscript.spt molecule.pdb
and you will see that the pdb is indeed not loaded.
> What am I doing wrong? Do these command line options work on the Mac?
It's not a Mac issue. I have the same in Windows
> PS Using
> $ jmol -s myscript.spt molecule.pdb
> provides the requested results, but it leaves Jmol open.
This is the clue: as I said, add "s" to "-ionx"
Once this is clear I will fix the Wiki
Bob, can we say that these 4 options are possible?
1) Jmol.jar molFileName
2) Jmol.jar scriptFileName
3) Jmol.jar -s scriptFileName
4) Jmol.jar -s scriptFileName molFileName
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